Biology homework and research

Copyright 2010 Catherine Hartkorn, Biol 211G A20, NMSU-A

Biology 211G A20: Online Cellular and Organismal Biology

Instructor: Catherine Hartkorn

Journal Club #2

GROUP ASSIGNMENT

(27 points for questions and 3 points for contribution = 30 points total)

Introduction

During Journal Club #1, you used a general internet search engine, a popular current

events magazine database, and the NMSU electronic journal database to find the assigned

TIME magazine article. Even though you were able to quickly locate the article via all

three methods, you noted that it is best to avoid finding scientific articles through general

internet search engines such as google because search results frequently include

questionable source websites, where the content of an original article may have been

altered.

Now, during this Journal Club #2, we will discuss reliable methods for finding scientific

journal articles that describe original experiments in biology. In particular, you will learn

how to use PubMed, an online biomedical literature database. We will also briefly

discuss various online resources that may be useful for you if you choose a health-related

or a biology-related career.

Assignment

PART I: (Not for submission)

Please complete this part on your own (without your group).

There is nothing to submit for this part of the assignment. However, you will need to

complete this part in order to do part II, which you will be submitting for a grade. Please

complete part I on your own - without your group members.

1. In Blackboard, under the Course Tools menu, click on the Web Links course tool.

Find the “Journal Club #2 Sites for Browsing” heading. First, read my descriptions for

each website listed under this heading, and then visit that website for a few minutes to get

an idea of what information each site contains. You do not need to look at any of these

sites in great detail. I just want you to understand the general purpose of each website.

Some of these resources may already be useful in your biology/health courses in your

program now; others may be useful for you later on in your biology/health-related career.

Copyright 2010 Catherine Hartkorn, Biol 211G A20, NMSU-A

2. Next, again under the Web Links course tool in Blackboard, find the “Journal Club #2

Sites for Tutorials” heading. Again, read the description of each site on this list, then go

to that site, and complete the specific online tutorials listed under each of the

corresponding descriptions. A list of which tutorials that you should complete is also

provided below. These tutorials will introduce you to two important biological

databases: NCBI's Entrez and PubMed. You will be using PubMed to complete Part II

of this assignment. Many of you will need to use these databases in your higher level

biology and biochemistry courses, especially if you choose to go to

graduate/medical/nursing school and/or have a career in biomedical research.

a) Go to:

http://www.ncbi.nlm.nih.gov/About/glance/programs.html

Read about the Programs and Activities of NCBI. You should learn what the NCBI is

and what it does.

b) Go to :

http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/

This should take you to PubMed Online Tutorial. Read the system requirements on the

welcome page before beginning your tutorial; make sure your computer meets these

requirements. Download any necessary software.

Under Introduction on the left, read the PubMed Overview and What’s In PubMed?

tutorials.

c) Go to:

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgibook=helppubmed&part=pubmedhelp

Under PubMed Quick Start, read answers to the following questions: (You do NOT

need to turn anything in for this part, just look over the answers to these.)

How do I search PubMed?

How do I search by author? How do I search by journal name?

How do I find a specific citation? I have some information such as the author, journal

name and the year the article was published.

Can you explain the search results?

Copyright 2010 Catherine Hartkorn, Biol 211G A20, NMSU-A

How do I display an abstract?

How can I get a copy of the article?

How can I save my results?

I retrieved too many citations. How can I focus my search?

Now, scroll down to Search Field Descriptions and Tags. Look at the table here - these

are search tag abbreviations which you can use to focus your search. For example, if you

search for “Williams [au]” you are going to get too many results, and you do not want to

search through all the articles to find the one that you want. Therefore, adding additional

search descriptions with tags would help you focus your search. For example,

“Williams[au], New Mexico State University[ad], 2010 [dp]” might be better.

By the way, if you just type in the information into the search window in PubMed

without the search tags (just like you would when performing a google search), you are

probably going to get the right article anyways. However, you should still try to use

appropriate search tags whenever you can because you may not find what you are looking

for if the system misinterprets the words in your query. For example, if you want to find

articles written by an MIT professor James Protein whose last name is Protein, you want

to search for “Protein [au] instead of “Protein;” otherwise, without the author search tag,

the search system will interpret the word “protein” as the type of biological molecule, and

your results will include a very large number of articles on structure and functioning of

various proteins.

Alternatively, you may also use the Limits function to focus your search, but I personally

find this function too cumbersome.

d) Next, go to:

http://www.nlm.nih.gov/bsd/disted/pubmed.html#qt

Under PubMed Quick Tours, please watch the following Searching PubMed tutorials:

 Search PubMed for an Author (3 min.)

 Searching PubMed by Author and Subject (1 min.)

 PubMed Simple Subject Search (1 min.)

 Search for a Journal (3 min.)

 Retrieving Citations from a Journal Issue (1 min.)

Now, let's practice what you have learned.

Copyright 2010 Catherine Hartkorn, Biol 211G A20, NMSU-A

PART II: (FOR SUBMISSION).

(27 points for questions and 3 points for contribution = 30 points total)

Please complete this part in your assigned GROUP. It is up to you and other students in

your group how you divide up the work. Only one copy of answers should be submitted

per group. Please designate one member to do this.

This assignment should be submitted under the Assignments course tool, Journal Club #2

assignment. Check the syllabus or the Assignments course tool for specific due date.

Also, it is up to you how you would like to “meet” with your group members. You may

either use the private DISCUSSION boards and CHAT rooms which the instructor set-up

for your group, or alternatively, you may email, call or meet your group members in

person. Your communications under your group's discussion board and chat room will

NOT be directly graded; however, the instructor may still use these to identify potential

contribution issues within your group.

a) First, go to:

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp

Question 1: Please list the search field tags you would use for the following

descriptions: (for example, from my above examples: affiliation [ad], author[au]):

(2 points)

journal title

language of the article

publication date

particular words in text

title of the article

particular words in the title and/or in abstract

volume number

issue number

b) Now, look back at the Time magazine article we read during Journal Club #1:

Cloud, John. Why your DNA isn’t your destiny, Time, Jan 18 2010 pp. 48-53.

On page 51, the author of the Time magazine discusses the Waterland and Jirtle 2003

study with agouti mice. Find this reference in this Time magazine article

Copyright 2010 Catherine Hartkorn, Biol 211G A20, NMSU-A

Using appropriate search descriptions and tags, find the above Waterland and Jirtle 2003

article through PubMed:

http://www.ncbi.nlm.nih.gov/pubmed

Question 2. List the search description/criteria and search tags you used to find the

above Waterland 2003 article. (1 point)

Question 3. Copy and paste the citation for the Waterland 2003 article here.

Explain what it contains. (2 points)

This is the proper way to cite a journal article, you should remember it for future use –

for instance, in the reference section of your disease/technique presentation in the 211

laboratory course.

However, be aware that often you do see slight variations in how articles are cited in

other journal articles, and that is fine too.

c) Next, in PubMed, click on the citation of this article to see the abstract for the

Waterland article.

Question 4. Copy and paste the abstract here. Explain what its purpose is. (2

points)

d) Click on the Free full text article in PubMed Central link on the right-hand side of the

screen. Often, PubMed provides links to free copies of articles directly through that

article's abstract pages. Remember that if a free copy of an article that you want to read

is not available, you can usually find a copy of this article through the online e-journal

database of the NMSU library.

e) Next, SKIM the Waterland and Jirtle 2003 article for organization; note the different

sections of this article, generally most journal articles (excluding review articles) follow

the same format or section division – although again frequently with some minor

variations.

Now, you do NOT need to understand everything in the article to be able to answer the

next several questions. For the purpose of this assignment, it is more important that you

Copyright 2010 Catherine Hartkorn, Biol 211G A20, NMSU-A

understand the general format of scientific journal articles than the various explanations

in this particular scientific journal article.

Question 5: List the main sections of this article (excluding title and authors,

acknowledgments/funding). Describe what the purpose of each section is or what

TYPE of general information it includes. Change between the HTML Full-text and

PDF format to see if one format is more clearly labeled. Also, please use your own

words; the simpler, the better. (6 points)

f) Finally, actually read the article to understand the study described in it. Again, you do

NOT need to understand everything in this article in order to be able to answer the

following questions. First, see if the abstract answers the question; however, if you do

not feel that the abstract answers that question then look in other sections of the article to

find the answer.

Normally, this is how a scientist would read a journal article: he/she would read the

abstract to get the main points about the experiment/study; then if he/she would like to

know more details, he/she would skim through the introduction and conclusion sections

and any descriptions under accompanying figures.

Typically, most scientists do not read the whole article because the results and

conclusions sections usually provide the most important information. However,

sometimes scientists may read the methods and materials section - especially if they want

to use or compare a method other scientists used with the method which they use in their

own research. Why spend time and money designing your own buffer or DNA extraction

method, when someone else already did and their method yields good results, right?

(rhetorical question :)

Answer the following questions about the Waterland 2003 article. Please be brief, you

do NOT need to write a lot here; one or two sentences will be enough to answer these

questions.

Question 6: (6 points)

What was the main goal/purpose of the experiment (what did the authors want to

accomplish here)?

What were the authors' prediction and hypothesis (what was the predicted outcome

of the experiment, why)?

How did they accomplish this (how did the authors test their hypothesis)?

Copyright 2010 Catherine Hartkorn, Biol 211G A20, NMSU-A

What were the results? How do they compare with the authors' original prediction?

What do the results mean in the greater scope of things (what were the authors'

conclusions about their results)?

g) Next, either in the PubMed citation view or in the full-text article view, on the right-

hand side of the screen, under the Related citations or PubMed related articles headings

respectively, find and go to the citation for the following review article:

J Nutr. 2006 Jun;136(6 Suppl):1706S-1710S. Assessing the effects of high methionine

intake on DNA methylation. Waterland RA.

(Note the different citation format here. If you cannot find this article in the related

citations window, please search PubMed for it directly.)

Next, click on the citation to see the abstract. Note that this article is a Review article.

When reading a review article, you need to keep in mind that many authors tend to

highlight their own research in their review articles; so you should always look at more

than one review article on a particular topic in your research to account for potential

personal biases.

Again, click on the free copy icon on the right-hand side of the screen.

SKIM through the article for organizational format; again, you do NOT need to fully read

this article to answer the following questions. As before, here also one or two sentences

are enough to answer these.

Question 7. What is the general purpose of a review article, and how does this

contrast with a non-review article? (1 point)

Question 8. List the main sections of this review article. Describe what the purpose

of each section is/what general information does it include. (6 points)

Copyright 2010 Catherine Hartkorn, Biol 211G A20, NMSU-A

Question 9. What does the author of this particular review article (Waterland 2006)

conclude about the effect of methionine supplementation on DNA methylation, and

DNA methylation's overall effect on human health: does the author say that DNA

methylation is detrimental and/or beneficial to the human health? Explain.

(1 point)

Again, I do NOT want to you to read the full article for this; I just want to show you that

you can find these answers very quickly if you know where to look. Journal articles are

internationally organized in a certain format for this exact purpose: because scientists do

not have enough time in a day to read scientific articles all day – they have to do their

own experiments too.

Conclusions

So, what did you learn from all of this? Let's go over this here:

Biological literature databases are very useful for finding and referencing information

that you may need as a scientist or as a doctor. These databases store citations for journal

articles on every imaginable biomedical research topic, frequently provide free abstracts

along with links to free full-text copies for each citation, and are convenient for locating

other articles that are related and/or cite a particular article.

PubMed is one – but VERY widely-used - such biomedical literature database: this

database stores citations and abstracts for BOTH non-review and review articles. Non-

review journal articles summarize results typically from one original experiment or study

conducted by the authors, meanwhile review journal articles summarize research progress

or what is known in a particular area of study based on several, past experiments

conducted either by the authors and/or other scientists.

However, the most important feature of large biological databases such as PubMed is that

they cross-reference information in their own databases with other biological databases

for such factors such as DNA and protein structure, protein function, DNA and protein

sequence similarity between different organisms, etc. This enables scientists to think

about their findings from many different angles: does gene sequence similarity mean that

this organism evolved from that other organism, does protein sequence similarity mean

that this protein has the same enzymatic function as another similar-in-sequence protein,

how can I use the known gene sequence to make the best possible primer for my PCR

reaction to amplify this particular part of the bacterial genome, etc.

So, for now the main take away message here is that: cross-referenced databases can help

answer a lot more questions than databases which are disconnected from other databases.

Copyright 2010 Catherine Hartkorn, Biol 211G A20, NMSU-A

But you will be learning a lot more about these databases in your higher level biology

courses at a later point in your science career – in particular, if you take Bioinformatics

courses.

Contribution Score

After your designated group member submits the assignment, ALL STUDENTS IN

THE COURSE need to email the instructor through Blackboard email with

contribution scores for yourself and your group members. If everyone contributed

equally, just say “all 3s”. If there were problems and you feel that someone did not

contribute equally to the assignment, please list each student by name and assign them a

score from 3 to 0 (with 3 providing valuable contribution, 2 some valuable contribution, 1

insufficient/very little contribution, and 0 not contributing at all). You may include

additional comments with your scores. Your emails will be confidential. Based on these

scores and if needed your discussion posts/chat group conversations about the

assignment, the instructor may penalize a student's score for this assignment.

As usual, let me know if you have any questions.